diff --git a/docs/Makefile b/docs/Makefile
index f5c964f..5309291 100644
--- a/docs/Makefile
+++ b/docs/Makefile
@@ -1,6 +1,6 @@
-# depends on pandoc (>= 2.0) and pdf2svg
+# depends on pandoc (>= 2.0) with pandoc-citeproc and pdf2svg
 
 all: model.html
 
-model.html: model.md style.css
-	pandoc --lua-filter tikz.lua --mathjax -s -o "$@" "$<" -c "$(word 2,$^)"
+model.html: model.md style.css references.bib
+	pandoc --filter pandoc-citeproc --lua-filter tikz.lua --mathjax -s -o "$@" "$<"
diff --git a/docs/council-of-science-editors-alphabetical.csl b/docs/council-of-science-editors-alphabetical.csl
new file mode 100644
index 0000000..9f2e2d2
--- /dev/null
+++ b/docs/council-of-science-editors-alphabetical.csl
@@ -0,0 +1,252 @@
+<?xml version="1.0" encoding="utf-8"?>
+<style xmlns="http://purl.org/net/xbiblio/csl" class="in-text" version="1.0" demote-non-dropping-particle="sort-only" default-locale="en-US">
+  <info>
+    <title>Council of Science Editors, Citation-Name (numeric, sorted alphabetically)</title>
+    <title-short>CSE C-N</title-short>
+    <id>http://www.zotero.org/styles/council-of-science-editors-alphabetical</id>
+    <link href="http://www.zotero.org/styles/council-of-science-editors-alphabetical" rel="self"/>
+    <link href="http://www.zotero.org/styles/council-of-science-editors" rel="template"/>
+    <link href="http://www.scientificstyleandformat.org/Tools/SSF-Citation-Quick-Guide.html" rel="documentation"/>
+    <author>
+      <name>Julian Onions</name>
+      <email>julian.onions@gmail.com</email>
+    </author>
+    <contributor>
+      <name>Patrick O'Brien</name>
+    </contributor>
+    <contributor>
+      <name>Aurimas Vinckevicius</name>
+      <email>aurimas.dev@gmail.com</email>
+    </contributor>
+    <category citation-format="numeric"/>
+    <category field="science"/>
+    <summary>The Council of Science Editors style 8th edition, Citation-Name system: numbers in text, sorted in alphabetical order by author.</summary>
+    <updated>2019-01-16T10:57:42+00:00</updated>
+    <rights license="http://creativecommons.org/licenses/by-sa/3.0/">This work is licensed under a Creative Commons Attribution-ShareAlike 3.0 License</rights>
+  </info>
+  <locale xml:lang="en">
+    <terms>
+      <term name="editortranslator" form="long">
+        <single>editor and translator</single>
+        <multiple>editors and translators</multiple>
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+        <single>editor</single>
+        <multiple>editors</multiple>
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+  <macro name="editor">
+    <names variable="editor translator" delimiter="; " suffix=".">
+      <name delimiter-precedes-last="always" initialize-with="" name-as-sort-order="all" sort-separator=" "/>
+      <label prefix=", "/>
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+    <names variable="author" delimiter="; ">
+      <name name-as-sort-order="all" sort-separator=" " initialize-with="" delimiter=", " delimiter-precedes-last="always"/>
+      <label form="long" prefix=", " strip-periods="true"/>
+      <substitute>
+        <names variable="editor translator"/>
+        <text variable="title"/>
+      </substitute>
+    </names>
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+    <group delimiter=". ">
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+    <choose>
+      <if variable="accessed" match="any">
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+      <text variable="title"/>
+      <choose>
+        <if type="thesis" match="any">
+          <text variable="genre" form="long" prefix="[" suffix="]"/>
+        </if>
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+  <macro name="publisher">
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+      <text variable="publisher"/>
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+      <date variable="issued" delimiter=" ">
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+        <if type="patent article-newspaper webpage" match="any">
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+          <date-part name="day"/>
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+  </macro>
+  <macro name="pages">
+    <group>
+      <label variable="page" form="short" suffix=" " plural="never"/>
+      <text variable="page"/>
+    </group>
+  </macro>
+  <macro name="edition">
+    <choose>
+      <if is-numeric="edition">
+        <group delimiter=" ">
+          <number variable="edition" form="ordinal"/>
+          <text term="edition" form="short"/>
+        </group>
+      </if>
+      <else>
+        <text variable="edition" suffix="."/>
+      </else>
+    </choose>
+  </macro>
+  <macro name="collection">
+    <choose>
+      <if type="report">
+        <group prefix=" " suffix="." delimiter=" ">
+          <text variable="collection-title"/>
+          <text variable="number" prefix=" Report No.: "/>
+        </group>
+      </if>
+      <else>
+        <group prefix=" (" suffix=")." delimiter=" ">
+          <names variable="collection-editor" suffix=". ">
+            <name delimiter-precedes-last="always" initialize-with="" name-as-sort-order="all" sort-separator=" "/>
+            <label prefix=", "/>
+          </names>
+          <text variable="collection-title"/>
+        </group>
+      </else>
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+  </macro>
+  <citation collapse="citation-number">
+    <sort>
+      <key variable="citation-number"/>
+    </sort>
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+      <text variable="citation-number"/>
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+        <label variable="locator" form="short" strip-periods="true"/>
+        <text variable="locator"/>
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+  <bibliography hanging-indent="false" et-al-min="11" et-al-use-first="10">
+    <sort>
+      <key macro="author"/>
+      <key variable="title"/>
+    </sort>
+    <layout>
+      <text variable="citation-number" suffix=". "/>
+      <text macro="author" suffix="."/>
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+        <if type="bill book graphic legal_case legislation motion_picture report song thesis" match="any">
+          <group prefix=" " suffix="." delimiter=" ">
+            <text macro="title" suffix="."/>
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+              <text macro="issued"/>
+              <text macro="pages"/>
+            </group>
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+        <else-if type="chapter paper-conference entry-dictionary entry-encyclopedia" match="any">
+          <text macro="title" prefix=" " suffix="."/>
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+            <group delimiter=" ">
+              <text term="in" text-case="capitalize-first" suffix=":"/>
+              <text macro="editor"/>
+              <text variable="container-title" suffix="."/>
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+            <group delimiter=" " suffix=".">
+              <label text-case="capitalize-first" variable="volume" form="short"/>
+              <text variable="volume"/>
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+              <text macro="publisher"/>
+              <group suffix="." delimiter=". ">
+                <text macro="issued"/>
+                <text macro="pages"/>
+              </group>
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+          </group>
+        </else-if>
+        <else-if type="review review-book" match="any">
+          <group suffix=".">
+            <text macro="title" prefix=" "/>
+            <text macro="editor" prefix=" "/>
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+              </group>
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+          <group suffix="." prefix=" " delimiter=". ">
+            <text macro="title"/>
+            <text macro="editor"/>
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+              <text macro="issued"/>
+              <group>
+                <text variable="volume"/>
+                <text variable="issue" prefix="(" suffix=")"/>
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+            <text variable="page" prefix=":"/>
+          </group>
+        </else>
+      </choose>
+      <text prefix=" " macro="collection"/>
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diff --git a/docs/model.html b/docs/model.html
index 0ef6126..f352ecf 100644
--- a/docs/model.html
+++ b/docs/model.html
@@ -4,7 +4,7 @@
   <meta charset="utf-8" />
   <meta name="generator" content="pandoc" />
   <meta name="viewport" content="width=device-width, initial-scale=1.0, user-scalable=yes" />
-  <title>model</title>
+  <title>ASt model description</title>
   <style>
       code{white-space: pre-wrap;}
       span.smallcaps{font-variant: small-caps;}
@@ -18,9 +18,11 @@
   <![endif]-->
 </head>
 <body>
-<h1 id="model-description">Model description</h1>
+<header id="title-block-header">
+<h1 class="title">ASt model description</h1>
+</header>
 <p>There are several approaches for dealing with neuropil contamination, the most common involve subtracting the surrounding neuropil fluorescence from each ROI with a scale factor determined by linear regression or hand-picked manually.</p>
-<p>We fit both ROI and surround fluorescence to asymmetric Student-t (ASt) distributions, whose mean was determined by a common neuropil signal contributing to both ROI and surrounding fluorescence:</p>
+<p>We fit both ROI and surround fluorescence to asymmetric Student-t (ASt) distributions,<span class="citation" data-cites="Zhu2010"><sup><a href="#ref-Zhu2010" role="doc-biblioref">4</a></sup></span> whose mean was determined by a common neuropil signal contributing to both ROI and surrounding fluorescence:</p>
 <p><span class="math display">\[\begin{align}
     f_r(t) &amp;\sim \mathrm{ASt}(\alpha z(t) + \mu_r, \sigma^2) \\
     f_n(t) &amp;\sim \mathrm{ASt}(z(t) + \mu_n, \sigma^2 / N) \\
@@ -31,10 +33,25 @@ <h1 id="model-description">Model description</h1>
 <p>The following figure represents the corresponding probabilistic graphical model, gray nodes indicating observed variables and white nodes latent variables.</p>
 <p><img src="f9420a611d0987ff66e9541d0ef5e35e0a98ed76.svg" /></p>
 <p>The advantage of this approach over other methods, lies in the use of the ASt distribution to model deviations in both ROI and surround signals. The long right tail of the ASt distribution helps prevent over-estimating the neuropil component for densely active cells. At the same time, the use of the ASt distribution for the surround signal helps account for transient increases in fluorescence arising from unannotated neurites or cell bodies, which could otherwise result in false negative transients in the corrected trace.</p>
-<p>The challenge of fitting this model is that the posterior distributions over model parameters, including the neuropil trace <span class="math inline">\(z(t)\)</span>, cannot be computed exactly. Instead, we use the black-box stochastic variational inference (BBSVI) with reparametrization gradients to fit an approximate posterior distribution.</p>
+<p>The challenge of fitting this model is that the posterior distributions over model parameters, including the neuropil trace <span class="math inline">\(z(t)\)</span>, cannot be computed exactly. Instead, we use the black-box stochastic variational inference (BBSVI) with reparametrization gradients<span class="citation" data-cites="Ranganath2014 Titsias2014 Kucukelbir2017"><sup><a href="#ref-Kucukelbir2017" role="doc-biblioref">1</a>–<a href="#ref-Titsias2014" role="doc-biblioref">3</a></sup></span> to fit an approximate posterior distribution.</p>
 <p>The neuropil corrected fluorescence trace will then be estimated as the “noise” of the ASt model:</p>
 <p><span class="math display">\[f(t) = f_r(t)- \hat{\alpha} \hat{z}(t)\]</span></p>
 <p>where <span class="math inline">\(\hat{\alpha}\)</span> and <span class="math inline">\(\hat{z}(t)\)</span> are point estimates derived from the approximate posterior distribution, e.g. its mean.</p>
 <p>The ASt model is not limited to finding common contaminating signals in two traces. In principle, we could split the neuropil donut into multiple sectors and provide a trace for each one of them. <code>fit_ast_model</code> can also correct for baseline drift as a part of the neuropil estimation procedure.</p>
+<h1 id="references" class="unnumbered">References</h1>
+<div id="refs" class="references" role="doc-bibliography">
+<div id="ref-Kucukelbir2017">
+<p>1. Kucukelbir A, Tran D, Ranganath R, Gelman A, Blei DM. Automatic differentiation variational inference. Journal of Machine Learning Research. 2017;18:14:1–14:45.</p>
+</div>
+<div id="ref-Ranganath2014">
+<p>2. Ranganath R, Gerrish S, Blei DM. Black box variational inference. In: Proceedings of the seventeenth international conference on artificial intelligence and statistics, AISTATS 2014, reykjavik, iceland, april 22-25, 2014. Vol. 33. JMLR.org; 2014. pp. 814–822. (JMLR workshop and conference proceedings).</p>
+</div>
+<div id="ref-Titsias2014">
+<p>3. Titsias MK, Yau C. Hamming ball auxiliary sampling for factorial hidden markov models. In: Ghahramani Z; Welling M; Cortes C; Lawrence ND; Weinberger KQ, editors. Advances in neural information processing systems 27: Annual conference on neural information processing systems 2014, december 8-13 2014, montreal, quebec, canada. 2014. pp. 2960–2968.</p>
+</div>
+<div id="ref-Zhu2010">
+<p>4. Zhu D, Galbraith JW. A generalized asymmetric student-t distribution with application to financial econometrics. Journal of Econometrics. 2010;157(2):297–305. doi:<a href="https://doi.org/10.1016/j.jeconom.2010.01.013">10.1016/j.jeconom.2010.01.013</a></p>
+</div>
+</div>
 </body>
 </html>
diff --git a/docs/model.md b/docs/model.md
index a18e0bd..26220b3 100644
--- a/docs/model.md
+++ b/docs/model.md
@@ -1,11 +1,17 @@
-# Model description
+---
+title: ASt model description
+bibliography: references.bib
+link-citations: true
+csl: council-of-science-editors-alphabetical.csl
+css: style.css
+---
 
 There are several approaches for dealing with neuropil contamination, the most
 common involve subtracting the surrounding neuropil fluorescence from each ROI
 with a scale factor determined by linear regression or hand-picked manually.
 
 We fit both ROI and surround fluorescence to asymmetric Student-t (ASt)
-distributions, whose mean was determined by a common neuropil signal
+distributions [@Zhu2010], whose mean was determined by a common neuropil signal
 contributing to both ROI and surrounding fluorescence:
 
 \begin{align}
@@ -56,7 +62,8 @@ otherwise result in false negative transients in the corrected trace.
 The challenge of fitting this model is that the posterior distributions over
 model parameters, including the neuropil trace $z(t)$, cannot be computed
 exactly. Instead, we use the black-box stochastic variational inference (BBSVI)
-with reparametrization gradients to fit an approximate posterior distribution.
+with reparametrization gradients [@Ranganath2014;@Titsias2014;@Kucukelbir2017]
+to fit an approximate posterior distribution.
 
 The neuropil corrected fluorescence trace will then be estimated as the "noise"
 of the ASt model:
@@ -70,3 +77,5 @@ The ASt model is not limited to finding common contaminating signals in two
 traces. In principle, we could split the neuropil donut into multiple sectors
 and provide a trace for each one of them. `fit_ast_model` can also correct for
 baseline drift as a part of the neuropil estimation procedure.
+
+# References
diff --git a/docs/references.bib b/docs/references.bib
new file mode 100644
index 0000000..8cec160
--- /dev/null
+++ b/docs/references.bib
@@ -0,0 +1,80 @@
+% This file was created with JabRef 2.10.
+% Encoding: UTF-8
+
+
+@InProceedings{Ranganath2014,
+  Title                    = {Black Box Variational Inference},
+  Author                   = {Rajesh Ranganath and Sean Gerrish and David M. Blei},
+  Booktitle                = {Proceedings of the Seventeenth International Conference on Artificial Intelligence and Statistics, {AISTATS} 2014, Reykjavik, Iceland, April 22-25, 2014},
+  Year                     = {2014},
+  Pages                    = {814--822},
+  Bibsource                = {dblp computer science bibliography, https://dblp.org},
+  Biburl                   = {https://dblp.org/rec/bib/conf/aistats/RanganathGB14},
+  Crossref                 = {DBLP:conf/aistats/2014},
+  Timestamp                = {Wed, 29 May 2019 08:41:44 +0200},
+  Url                      = {http://proceedings.mlr.press/v33/ranganath14.html}
+}
+
+@InProceedings{Titsias2014,
+  Title                    = {Hamming Ball Auxiliary Sampling for Factorial Hidden Markov Models},
+  Author                   = {Michalis K. Titsias and Christopher Yau},
+  Booktitle                = {Advances in Neural Information Processing Systems 27: Annual Conference on Neural Information Processing Systems 2014, December 8-13 2014, Montreal, Quebec, Canada},
+  Year                     = {2014},
+  Pages                    = {2960--2968},
+  Bibsource                = {dblp computer science bibliography, https://dblp.org},
+  Biburl                   = {https://dblp.org/rec/bib/conf/nips/TitsiasY14},
+  Crossref                 = {DBLP:conf/nips/2014},
+  Timestamp                = {Wed, 10 Dec 2014 21:34:12 +0100},
+  Url                      = {http://papers.nips.cc/paper/5456-hamming-ball-auxiliary-sampling-for-factorial-hidden-markov-models}
+}
+
+@Article{Kucukelbir2017,
+  Title                    = {Automatic Differentiation Variational Inference},
+  Author                   = {Alp Kucukelbir and Dustin Tran and Rajesh Ranganath and Andrew Gelman and David M. Blei},
+  Journal                  = {Journal of Machine Learning Research},
+  Year                     = {2017},
+  Pages                    = {14:1--14:45},
+  Volume                   = {18},
+  Bibsource                = {dblp computer science bibliography, https://dblp.org},
+  Biburl                   = {https://dblp.org/rec/bib/journals/jmlr/KucukelbirTRGB17},
+  Timestamp                = {Wed, 03 Apr 2019 18:34:04 +0200},
+  Url                      = {http://jmlr.org/papers/v18/16-107.html}
+}
+
+@Article{Zhu2010,
+  Title                    = {A generalized asymmetric Student-t distribution with application to financial econometrics},
+  Author                   = {Dongming Zhu and John W. Galbraith},
+  Journal                  = {Journal of Econometrics},
+  Year                     = {2010},
+  Number                   = {2},
+  Pages                    = {297 - 305},
+  Volume                   = {157},
+  Abstract                 = {This paper proposes a new class of asymmetric Student-t (AST) distributions, and investigates its properties, gives procedures for estimation, and indicates applications in financial econometrics. We derive analytical expressions for the cdf, quantile function, moments, and quantities useful in financial econometric applications such as the Expected Shortfall. A stochastic representation of the distribution is also given. Although the AST density does not satisfy the usual regularity conditions for maximum likelihood estimation, we establish consistency, asymptotic normality and efficiency of ML estimators and derive an explicit analytical expression for the asymptotic covariance matrix. A Monte Carlo study indicates generally good finite-sample conformity with these asymptotic properties.},
+  Doi                      = {10.1016/j.jeconom.2010.01.013},
+  ISSN                     = {0304-4076},
+  Keywords                 = {Asymmetric distribution, Expected Shortfall, Maximum likelihood estimation},
+  Url                      = {http://www.sciencedirect.com/science/article/pii/S0304407610000266}
+}
+
+@Proceedings{DBLP:conf/nips/2014,
+  Title                    = {Advances in Neural Information Processing Systems 27: Annual Conference on Neural Information Processing Systems 2014, December 8-13 2014, Montreal, Quebec, Canada},
+  Year                     = {2014},
+  Editor                   = {Zoubin Ghahramani and Max Welling and Corinna Cortes and Neil D. Lawrence and Kilian Q. Weinberger},
+  Bibsource                = {dblp computer science bibliography, https://dblp.org},
+  Biburl                   = {https://dblp.org/rec/bib/conf/nips/2014},
+  Timestamp                = {Wed, 10 Dec 2014 21:34:12 +0100},
+  Url                      = {http://papers.nips.cc/book/advances-in-neural-information-processing-systems-27-2014}
+}
+
+@Proceedings{DBLP:conf/aistats/2014,
+  Title                    = {Proceedings of the Seventeenth International Conference on Artificial Intelligence and Statistics, {AISTATS} 2014, Reykjavik, Iceland, April 22-25, 2014},
+  Year                     = {2014},
+  Publisher                = {JMLR.org},
+  Series                   = {{JMLR} Workshop and Conference Proceedings},
+  Volume                   = {33},
+  Bibsource                = {dblp computer science bibliography, https://dblp.org},
+  Biburl                   = {https://dblp.org/rec/bib/conf/aistats/2014},
+  Timestamp                = {Wed, 29 May 2019 08:41:44 +0200},
+  Url                      = {http://proceedings.mlr.press/v33/}
+}
+